Misc Skills

Fixing Albacore 5-line FASTQ

Albacore FASTQ has the odd blank line in it which breaks a lot of software tools. To get rid of this, something like:

grep . albacore.fastq > fixed.fastq

If you have a bunch of FASTQ files from albacore, try:

cat *.fastq | grep . > fixed.combined.fastq

Extracting a sequence from a multi-fasta

If you want to extract a single sequence from a FASTA file, we can do this with samtools faidx.

First we need to index the file:

samtools faidx myreads.fasta

Then we can extract a single entry using the ID of the sequence

samtools faidx myreads.fasta 51a62194-76d1-4dbb-bbf0-1548f18857a6_Classification_2d:2D_000:2d